A biomarker is generally a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes or pharmacological responses to a therapeutic intervention. See Atkinson et al., 2001, Clin. Pharmacol. Ther. 69:89-95. Biomarkers vary widely in nature, ease of measurement and correlation with physiological states of interest. See, e.g., Frank et al., 2003, Nature Reviews Drug Discovery 2:566-580. It is widely believed that the development of new validated biomarkers will lead both to significant reductions in healthcare and drug development costs and to significant improvements in treatment for a wide variety of diseases and conditions. Thus, a great deal of effort has been directed to using new technologies to find new classes of biomarkers. See, e.g., Petricoin et al., 2002, Nature Reviews Drug Discovery, 1:683-695; and Sidransky, 2002, Nature Reviews Cancer 2:210-219.
The interactions of cell surface membrane components play crucial roles in transmitting extracellular signals to a cell in normal physiology and in disease conditions. In particular, many types of cell surface receptors undergo dimerization, oligomerization or clustering in connection with the transduction of an extracellular event or signal into a cellular response, such as, e.g., proliferation, increased or decreased gene expression or the like. See, e.g., George et al., 2002, Nature Reviews Drug Discovery 1:808-820; Mellado et al, 2001, Ann. Rev. Immunol. 19:397-421; Schlessinger, 2000, Cell 103:211-225; and Yarden, 2001, Eur. J. Cancer 37:S3-S8. The role of such events in diseases, such as cancer, has been the object of intense research and has led to the development of several new drugs and drug candidates. See, e.g., Herbst and Shin, 2002, Cancer 94:1593-1611; Yarden and Sliwkowski, 2001, Nature Reviews Molecular Cell Biology 2:127-137; McCormick, 1999, Trends in Cell Biology 9:53-56 (1999); and Blume-Jensen and Hunter, 2001, Nature 411:355-365.
Expression levels of individual cell surface receptors, such as Her-2, have been used as biomarkers. Conventional immunohistochemical (IHC) or fluorescence in situ hybridization (FISH) analysis has been used to detect Her-2 overexpression to determine whether treatment with a Her2-acting agent, e.g., trastuzumab, is warranted. Also, U.S. Pat. No. 4,968,603 describes Her-2 expression as a cancer biomarker. However, in two different studies, only 20% or 35% of patients overexpressing Her-2 objectively responded to trastuzumab treatment. See Baselga et al., 1996, J. Clin. Oncol. 14:737-44; Cobleigh et al., 1999, J. Clin. Oncol. 17:2639-48; and Vogel et al., 2002, J. Clin. Oncol. 20:719-26. Further, in other studies of the combination of trastuzumab plus chemotherapy in the metastatic breast cancer setting, only approximately 50% of patients overexpressing Her-2 objectively responded to trastuzumab combination therapy. See Slamon et al. N Engl J Med 344: 783-92.
At the current time, there is no method that can reliably determine whether a subject with a cancer is likely or unlikely to respond to treatment with a Her-2-acting agent, such as trastuzumab. Such a method may be used to identify patients unlikely to respond to trastuzumab and avoid providing costly treatment to those patients. Such an assay may also be used to identify patients that are unlikely to respond to a chemotherapeutic agent in addition to the Her-2 acting agent thus allowing the subject to avoid the potentially toxic effects of the chemotherapeutic agent. Such a method may also be used to predict a time course of disease or a probability of a significant event in the disease for Her-2 positive patients.